annotate test-data/summary/nsp8.PRIME.json @ 23:840b5fec0de9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"

{
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      ]
    },
   "headers":    [
["alpha;", "Synonymous substitution rate at a site"],
    ["β", "Log of property independent non-synonymous rate a site"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
    ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
    ["FEL LogL", "Site Log-likelihood under the FEL model"],
    ["p-value", "Omnibus p-value (any property is important)"],
    ["λ1", "Importance for Factor I bipolar"],
    ["p1", "p-value for non-zero effect of Factor I bipolar"],
    ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
    ["λ2", "Importance for Factor II secondary structure"],
    ["p2", "p-value for non-zero effect of Factor II secondary structure"],
    ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
    ["λ3", "Importance for Factor III volume"],
    ["p3", "p-value for non-zero effect of Factor III volume"],
    ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
    ["λ4", "Importance for Factor IV composition"],
    ["p4", "p-value for non-zero effect of Factor IV composition"],
    ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
    ["λ5", "Importance for Factor V charge"],
    ["p5", "p-value for non-zero effect of Factor V charge"],
    ["LogL5", "Log likelihood when there is no effect of Factor V charge"] 
    ]
  },
 "analysis":{
   "authors":"Sergei L. Kosakovsky Pond",
   "citation":"TBD",
   "contact":"[e-mail]",
   "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n    fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n    properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n    When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n    At each site, N tests are performed\n    A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis.\n    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"0.0.1"
  },
 "branch attributes":{
   "0":{
     "Node20":{
       "Global MG94xREV":0.001634412628363601,
       "Nucleotide GTR":0.001684521619549293
      },
     "Node38":{
       "Global MG94xREV":0.001735516181127408,
       "Nucleotide GTR":0.00168484920326581
      },
     "Node4":{
       "Global MG94xREV":0.001634082125054255,
       "Nucleotide GTR":0.001683801387489096
      },
     "REFERENCE":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"REFERENCE"
      },
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"
      },
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
       "Global MG94xREV":0.001732287226413535,
       "Nucleotide GTR":0.001682745450340891,
       "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"
      },
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021"
      },
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
       "Global MG94xREV":0.001731614558297581,
       "Nucleotide GTR":0.00168274558227101,
       "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021"
      },
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
       "Global MG94xREV":0.001735723689760284,
       "Nucleotide GTR":0.001684401404203384,
       "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021"
      },
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
       "Global MG94xREV":0.001732400224923104,
       "Nucleotide GTR":0.00168406792173386,
       "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021"
      },
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
       "Global MG94xREV":0.001734572372218793,
       "Nucleotide GTR":0.001684975469042935,
       "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021"
      },
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
       "Global MG94xREV":0.001735567212797747,
       "Nucleotide GTR":0.001684401583391051,
       "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021"
      },
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
       "Global MG94xREV":0.001732287290600434,
       "Nucleotide GTR":0.001682745512695379,
       "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021"
      },
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021"
      },
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
       "Global MG94xREV":0.001733756929863212,
       "Nucleotide GTR":0.001684431017860219,
       "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021"
      },
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
       "Global MG94xREV":0.001733765372843661,
       "Nucleotide GTR":0.001684439221071522,
       "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021"
      },
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021"
      },
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
       "Global MG94xREV":0.001736016199323374,
       "Nucleotide GTR":0.00168443927661716,
       "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021"
      },
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
       "Global MG94xREV":0.001733699172098583,
       "Nucleotide GTR":0.001685171120971631,
       "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021"
      },
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
       "Global MG94xREV":0.001733317353440973,
       "Nucleotide GTR":0.001684401899924961,
       "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021"
      },
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
       "Global MG94xREV":0.01050948249155059,
       "Nucleotide GTR":0.01020457779555702,
       "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human"
      },
     "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.02683667579915389,
       "Nucleotide GTR":0.02592331511084145,
       "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human"
      },
     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.005257318382497578,
       "Nucleotide GTR":0.005093980037543817,
       "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human"
      },
     "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003479916215882181,
       "Nucleotide GTR":0.003379296026417724,
       "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human"
      },
     "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003464849064677958,
       "Nucleotide GTR":0.003372774424630234,
       "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human"
      },
     "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.00347332934630856,
       "Nucleotide GTR":0.003374190595560375,
       "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human"
      },
     "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.00521423750425419,
       "Nucleotide GTR":0.00505933790460295,
       "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human"
      },
     "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003464011560303172,
       "Nucleotide GTR":0.003373764235314068,
       "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human"
      },
     "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.005236219925335357,
       "Nucleotide GTR":0.005068409188375663,
       "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human"
      },
     "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.003464842721718857,
       "Nucleotide GTR":0.003372774424770855,
       "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human"
      },
     "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
       "Global MG94xREV":0.001735902729272567,
       "Nucleotide GTR":0.001686266012390882,
       "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human"
      },
     "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003480097445990996,
       "Nucleotide GTR":0.003374436490976879,
       "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human"
      },
     "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003472571047451632,
       "Nucleotide GTR":0.003376034743011948,
       "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human"
      },
     "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003474988463696198,
       "Nucleotide GTR":0.003374190741831846,
       "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human"
      },
     "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
       "Global MG94xREV":0.003471294880575992,
       "Nucleotide GTR":0.003376937492543959,
       "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human"
      }
    },
   "attributes":{
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197] 
      ],
     "name":"prime.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":2512.962001128159,
     "Equilibrium frequencies":      [
[0.03825952761243274],
      [0.01370948533169502],
      [0.0238326285579188],
      [0.05169206288834598],
      [0.02910782227384961],
      [0.01043016700423795],
      [0.01813184740308045],
      [0.03932728586627101],
      [0.01035067712195123],
      [0.003708944282165923],
      [0.006447644771501305],
      [0.01398469573761802],
      [0.0283653688047424],
      [0.01016412464618009],
      [0.01766935821790241],
      [0.03832416445281453],
      [0.01521889661505549],
      [0.005453366858635389],
      [0.009480156518454269],
      [0.02056209812326697],
      [0.01157852606970437],
      [0.004148917752546374],
      [0.007212496554133422],
      [0.01564363009947405],
      [0.00411729822204095],
      [0.001475345962268018],
      [0.002564747797779777],
      [0.005562840210150803],
      [0.01128319250724396],
      [0.004043091272315801],
      [0.007028527343480687],
      [0.01524460789411934],
      [0.03592403244011121],
      [0.01287261047188149],
      [0.02237780168434643],
      [0.04853659885475865],
      [0.02733097915424774],
      [0.009793473186905268],
      [0.01702501611901085],
      [0.03692661100139533],
      [0.009718835644621534],
      [0.003482537371104292],
      [0.0060540580187001],
      [0.01313102107355921],
      [0.02663384763763138],
      [0.009543670983435077],
      [0.01659075888876379],
      [0.0359847236220365],
      [0.00848480075962617],
      [0.03199221880690793],
      [0.01801483181642438],
      [0.006455230577911434],
      [0.01122180073845716],
      [0.02433965804833868],
      [0.002295465694104339],
      [0.003990447484454917],
      [0.008655128485630147],
      [0.01755532734880559],
      [0.00629057695692368],
      [0.01093556617204019],
      [0.02371882618448924] 
      ],
     "Log Likelihood":-1205.058976375664,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.4929148115989916, 1] 
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[24.3195468932995, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":51
    },
   "Nucleotide GTR":{
     "AIC-c":2633.0046471406,
     "Equilibrium frequencies":      [
[0.3251262626262627],
      [0.1799242424242424],
      [0.2026515151515151],
      [0.2922979797979798] 
      ],
     "Log Likelihood":-1247.247280799152,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
       "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
       "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
       "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
      },
     "display order":0,
     "estimated parameters":69
    }
  },
 "input":{
   "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
   "number of sequences":32,
   "number of sites":198,
   "partition count":1,
   "trees":{
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    }
  },
 "tested":{
   "0":{
     "Node20":"test",
     "Node38":"background",
     "Node4":"test",
     "REFERENCE":"background",
     "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
     "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
     "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
     "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
     "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
     "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
     "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
     "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
     "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
     "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
     "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
     "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
     "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",
     "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
     "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
     "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
     "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
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     "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
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  },
 "timers":{
   "Model fitting":{
     "order":1,
     "timer":5
    },
   "PRIME analysis":{
     "order":2,
     "timer":19
    },
   "Total time":{
     "order":0,
     "timer":25
    }
  }
}